I've just done my first q-RT PCR using an ABI 7900HT and primer sets and probes specific for my gene and the 18S control.
In my samples I have a wild type and a number of derivatives that have been infected with a knock down construct.
I have calculated CT values for the gene and for the 18S (internal control). Then subtracted the CT(18S) from CT(gene) in each sample. This gave deltaCT figures of about 14. I then subtracted the deltaCT for the wildtype from the deltaCT for each knockdown sample to get a deltadeltaCT value. The largest knockdown gave a value of 2.4
The final stage is to calculate 2 to the power of deltadeltaCT for each, so for the best knockdown this gave 0.187025, whilst the wildtype control has the value 1.0
The question is: Can I now say that this sample has had the gene of interest knocked down by about 81%?